From owner-chemistry@ccl.net Wed Dec  6 02:12:00 2006
From: "DE BRUIN Theodorus theodorus.DE-BRUIN[*]IFP.fr" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: Density functionals for CO molecule
Message-Id: <-33188-061205170525-31680-kH/abzyOUpTCWLbfc9pT2w .. server.ccl.net>
X-Original-From: "DE BRUIN Theodorus" <theodorus.DE-BRUIN*|*IFP.fr>
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Date: Tue, 5 Dec 2006 16:14:31 +0100
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Sent to CCL by: "DE BRUIN Theodorus" [theodorus.DE-BRUIN^-^IFP.fr]

Dear CCLers

It seems that some density functionals are not well predicting the dipole moment of the CO molecule. Although the magnitude has the correct order, the direction is wrong (oxygen atom is carrying the negative charge instead of the carbon atom). Moreover, upon increasing the basis set, e.g. from triple zeta to aug-cc-pvtz, the direction of the dipole may change as well.

Could anyone of you point me to some articles in which functionals (and basis sets) were systematically tested for the CO molecule?

Thanks in advance,
Kind regards,
Theo de Bruin

--------
Theodorus de Bruin
Institut Français du Pétrole
Direction Chimie et Physico-Chimie Appliquées
Département Thermodynamique et Modélisation Moléculaire
1 & 4 Avenue de bois Préau
92852 Rueil-Malmaison Cedex
Tel: +33 (0)1.47.52.54.38
Fax: +33 (0)1.47.52.70.58 

__________________________

Ce message (et toutes ses pièces jointes éventuelles) est confidentiel et établi à l'intention exclusive de ses destinataires. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse. L'IFP décline toute responsabilité au titre de ce message.

This message and any attachments (the message) are confidential and intended solely for the addressees. Any unauthorised use or dissemination is prohibited. IFP should not be liable for this message.

Visitez notre site Web / Visit our web site : http://www.ifp.fr
__________________________


From owner-chemistry@ccl.net Wed Dec  6 03:39:00 2006
From: "allouche allouche*|*lasim.univ-lyon1.fr" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Freeware for building peptides
Message-Id: <-33189-061206032846-30456-wVyHGiFQEfUrpTWJ8TpocA=-=server.ccl.net>
X-Original-From: allouche <allouche|a|lasim.univ-lyon1.fr>
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Date: Wed, 06 Dec 2006 08:50:41 +0100
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Sent to CCL by: allouche [allouche.,,.lasim.univ-lyon1.fr]
Dear CCLers,

Gabedit software (free downloadable from http://gabedit.sourceforge.net) 
includes a molecular builder which can build peptides.
Gabedit work under Windows, Linux and Mac OS X11.

A.R. Allouche


>>Hello CCLers,
>>
>>I'm looking for a freewrare for windows/linux( an web server will do
>>too) to build up peptides,particularly small helical peptides similar to 
>>what  ACCELRYS BIOPOLYMER module can do.
>>    
>>


From owner-chemistry@ccl.net Wed Dec  6 04:14:00 2006
From: "Massimo Ottonelli massimo*chimica.unige.it" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: conversion of seconds to atomic mass units
Message-Id: <-33190-061205103705-721-Nf7/pSDarmhUDSuEnDy/OQ * server.ccl.net>
X-Original-From: Massimo Ottonelli <massimo#chimica.unige.it>
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Date: Tue, 05 Dec 2006 15:49:41 +0100
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Sent to CCL by: Massimo Ottonelli [massimo..chimica.unige.it]

my 2 cent:

  E = m c^2
  E = h  ni  =  h/ T
  so
  T = h / c^2 * 1/m

where c = speed of ligth and h Planck constant.

  Regards
  Massimo



At 09.13 05/12/2006 -0500, you wrote:
>Sent to CCL by: "CCL CCL" [computationalchemist%gmail.com]
>------=_Part_6546_26040142.1165322825902
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>dear folks,
>I know this is very naive question, but still i couldnt get answer. I'm
>wondering how to convert seconds to atomic mass units.
>Any suggestions will be greatly appreciated.
>--
>Regards,
>Dr. Sanjay
>
>------=_Part_6546_26040142.1165322825902
>Content-Type: text/html; charset=ISO-8859-1
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
><div>dear folks,</div>
><div>I know this is very naive question, but still i couldnt get answer. 
>I'm wondering how to convert seconds to atomic mass units. </div>
><div>Any suggestions will be greatly appreciated.<br>-- 
><br>Regards,<br>Dr. Sanjay </div>
>
>------=_Part_6546_26040142.1165322825902--

From owner-chemistry@ccl.net Wed Dec  6 06:47:00 2006
From: "kevin abbot kevanabbot*|*yahoo.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Freeware for building peptides
Message-Id: <-33191-061205075303-8487-i9RZM/+66KUIOqYenAwodQ^^server.ccl.net>
X-Original-From: kevin abbot <kevanabbot]|[yahoo.com>
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Date: Tue, 5 Dec 2006 03:52:50 -0800 (PST)
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Sent to CCL by: kevin abbot [kevanabbot-$-yahoo.com]

--0-1386979113-1165319570=:36328
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Hi,=0Atry Discovery Studio by  Accelrys. You can donwload it free of charge=
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ad><body><div style=3D"font-family:times new roman, new york, times, serif;=
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imes, serif"><BR><BR>&nbsp;</DIV>=0A<DIV style=3D"FONT-SIZE: 12pt; FONT-FAM=
ILY: times new roman, new york, times, serif">----- Original Message ----<B=
R>From: "Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com" &lt;owner-chemistry _ ccl.n=
et&gt;<BR>To: "Abbot, Kevin " &lt;kevanabbot _ yahoo.com&gt;<BR>Sent:=
 Tuesday, December 5, 2006 11:08:36 AM<BR>Subject: CCL: Freeware for buildi=
ng peptides<BR><BR>=0A<DIV>Sent to CCL by: "Itna&nbsp;&nbsp;Kcolc" [a_n_t_i=
_c_l_o_c_k(0)yahoo.com]<BR>Hello CCLers,<BR><BR>I'm looking for a freewrare=
 for windows/linux( an web server will do<BR>too) to build up peptides,part=
icularly small helical peptides similar to what&nbsp;&nbsp;ACCELRYS BIOPOLY=
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From owner-chemistry@ccl.net Wed Dec  6 08:39:01 2006
From: "Agalya G agalya81=gmail.com" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL: Oscillator strength
Message-Id: <-33192-061206083555-27338-554A4mNhGfU5d+v3ygu7tA!A!server.ccl.net>
X-Original-From: "Agalya  G" <agalya81---gmail.com>
Date: Wed, 6 Dec 2006 08:35:55 -0500


Sent to CCL by: "Agalya  G" [agalya81(!)gmail.com]
Hello all,


I want to calculate oscillator strength value for spin-forbidden transitions from singlet to triplet excited states. Is there any method which uses spin-orbit coupling to estimate the oscillator strength. 

Please give me some suggestions and guidance.

Thanks,
Agalya


From owner-chemistry@ccl.net Wed Dec  6 09:23:00 2006
From: "venkat karanam dodaghatta dkvenkata_rao()yahoo.co.in" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: Computational biology
Message-Id: <-33193-061205124520-8324-Gs02Pu6aVkGz2IDVRHJkRg_+_server.ccl.net>
X-Original-From: "venkat karanam dodaghatta" <dkvenkata_rao###yahoo.co.in>
Date: Tue, 5 Dec 2006 12:45:20 -0500


Sent to CCL by: "venkat karanam dodaghatta" [dkvenkata_rao]^[yahoo.co.in]

Dear sir,


I am Venkata Rao.D.K from India doing doctoral studies in computational biophysics. as a part of my research I have calculated lennard-jones potential between hydrophobic groups. my basic doubt is that can we define lennard-jones potential as hydrophobic energies or it is just approximation of vander waal interaction energies?.

is there any method to calculate hydrophobic interaction energies and any method to calculate continuum hydrophobic energies of energy files generated from MD.

please clarify my doubts




> From
VENKATA RAO.D.K
Dept of Microbiology
Sri Krishnadevaraya University
ANANTAPUR-515001
INDIA

E-mail: dkvenkata_rao!A!yahoo.co.in
        dkvenkata_rao!A!sancharnet.in


From owner-chemistry@ccl.net Wed Dec  6 12:32:01 2006
From: "Tammy Welshman compchem|hotmail.com" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL:G: PCM question
Message-Id: <-33194-061206122935-2880-AfekVybx4JLRcjO5vR2dCA+/-server.ccl.net>
X-Original-From: "Tammy  Welshman" <compchem .. hotmail.com>
Date: Wed, 6 Dec 2006 12:29:35 -0500


Sent to CCL by: "Tammy  Welshman" [compchem{}hotmail.com]
Hi all,

I am planning to use PCM in G03 to add solvent to the transition state of an SN2 reaction. The solvent, DMF, is not "available" in G03, so I need to input at least the dielectric (36.71), the solvent density (0.95 g/cm**3), and the solvent radius. The problem is the latter; I have found numerous values in the literature for the solvent radius of DMF ("RSolv" in G03), ranging from 2.44 Ang to 3.91 Ang. Hardly any of them give details on the origin or method of calculation for their respective RSolv values.

Does anyone have any ideas/solutions/refs pertaining to using DMF in PCM?? I am aware that I can calculate the solvent radius myself, but I wonder about the inconsistencies in the literature. Any help would be appreciated.

Thanx in advance,
Tammy

Tammy Welshman
Dept. of Chemistry
University of Manitoba
Winnipeg, Manitoba, Canada


From owner-chemistry@ccl.net Wed Dec  6 13:07:00 2006
From: "Mark Thompson mark ~~ arguslab.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Freeware for building peptides
Message-Id: <-33195-061205185055-24175-nhhKhNY6qkohFTBnog9mmQ.@.server.ccl.net>
X-Original-From: Mark Thompson <mark]![arguslab.com>
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Date: Tue, 05 Dec 2006 14:58:02 -0800
MIME-Version: 1.0


Sent to CCL by: Mark Thompson [mark*arguslab.com]

Hi Itna,
Not sure if this is what you are looking for.....
ArgusLab has a simple tool that allows you to specify phi,psi angles and 
build peptides interactively.
www.arguslab.com
Mark Thompson

Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com wrote:
> Sent to CCL by: "Itna  Kcolc" [a_n_t_i_c_l_o_c_k(0)yahoo.com]
> Hello CCLers,
>
> I'm looking for a freewrare for windows/linux( an web server will do
> too) to build up peptides,particularly small helical peptides similar to what  ACCELRYS BIOPOLYMER module can do.
>
> Thanks in advance>
>
>
>
>
>
>   

-- 



************************************
Mark Thompson
Planaria Software LLC
http://www.arguslab.com
mark|a|arguslab.com
************************************


From owner-chemistry@ccl.net Wed Dec  6 13:41:00 2006
From: "Jeff Hammond jeff.science(0)gmail.com" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: Density functionals for CO molecule
Message-Id: <-33196-061206104722-21279-+2qddkiM/kaSHNq/67bhLQ(~)server.ccl.net>
X-Original-From: "Jeff Hammond" <jeff.science ~ gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Wed, 6 Dec 2006 08:43:09 -0600
MIME-Version: 1.0


Sent to CCL by: "Jeff Hammond" [jeff.science---gmail.com]
Most SCF-based calculations, which includes DFT, do not get the sign
right, as you discovered.  Here are few papers which study the CO
dipole moment, but only the first has a DFT number.  The rest should
give you pause about believing DFT will ever succeed for this system.

LDA: P. Duffy, D. P. Chong and M. Dupuis, J. Chem. Phys. 102, 3312 (1995)
MRCI: J.F. Harrison, J. Phys. Chem. A 110, 10848-10857 (2006).
CC/MP: Scuseria, et. al, J. Chem. Phys. 94, 6660-6663 (1991)
CC/MP:K.A. Peterson and T.H. Dunning, Theochem 400, 93 (1997)

Jeff

On 12/6/06, DE BRUIN Theodorus theodorus.DE-BRUIN[*]IFP.fr
<owner-chemistry[#]ccl.net> wrote:
> Sent to CCL by: "DE BRUIN Theodorus" [theodorus.DE-BRUIN^-^IFP.fr]
>
> Dear CCLers
>
> It seems that some density functionals are not well predicting the dipole moment of the CO molecule. Although the magnitude has the correct order, the direction is wrong (oxygen atom is carrying the negative charge instead of the carbon atom). Moreover, upon increasing the basis set, e.g. from triple zeta to aug-cc-pvtz, the direction of the dipole may change as well.
>
> Could anyone of you point me to some articles in which functionals (and basis sets) were systematically tested for the CO molecule?
>
> Thanks in advance,
> Kind regards,
> Theo de Bruin
>
> --------
> Theodorus de Bruin
> Institut Français du Pétrole
> Direction Chimie et Physico-Chimie Appliquées
> Département Thermodynamique et Modélisation Moléculaire
> 1 & 4 Avenue de bois Préau
> 92852 Rueil-Malmaison Cedex
> Tel: +33 (0)1.47.52.54.38
> Fax: +33 (0)1.47.52.70.58
>
> __________________________
>
> Ce message (et toutes ses pièces jointes éventuelles) est confidentiel et établi à l'intention exclusive de ses destinataires. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse. L'IFP décline toute responsabilité au titre de ce message.
>
> This message and any attachments (the message) are confidential and intended solely for the addressees. Any unauthorised use or dissemination is prohibited. IFP should not be liable for this message.
>
> Visitez notre site Web / Visit our web site : http://www.ifp.fr
> __________________________>
>
>
>



-- 
Jeff Hammond
The University of Chicago


From owner-chemistry@ccl.net Wed Dec  6 16:45:00 2006
From: "Patrizia Calaminici pcalamin]*[mercurio.red.cinvestav.mx" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: Density functionals for CO molecule
Message-Id: <-33197-061206152831-11188-fAk8N7SQ+Ho41dsU/oCgAQ-.-server.ccl.net>
X-Original-From: Patrizia Calaminici <pcalamin-x-mercurio.red.cinvestav.mx>
Content-Transfer-Encoding: 8BIT
Content-Type: TEXT/PLAIN; charset=ISO-8859-1
Date: Wed, 6 Dec 2006 13:24:58 -0600 (CST)
MIME-Version: 1.0


Sent to CCL by: Patrizia Calaminici [pcalamin=mercurio.red.cinvestav.mx]


Dear Theodorus de Bruin and dear CCLers,

Please give a look at the following reference,

P. Calaminici, K. Jug, A.M. Koster, J. Chem. Phys. 109 (18), 7756 1998,

which shows that reliable dipole moment can be obtained for the
CO molecule if DFT calculations using basis sets explicitally 
optimized for this level of theory would be employed.

Hoping this will help.

Kind regards,

                     Patrizia Calaminici
                  

On Wed, 6 Dec 2006, Jeff Hammond jeff.science(0)gmail.com wrote:

> Sent to CCL by: "Jeff Hammond" [jeff.science---gmail.com]
> Most SCF-based calculations, which includes DFT, do not get the sign
> right, as you discovered.  Here are few papers which study the CO
> dipole moment, but only the first has a DFT number.  The rest should
> give you pause about believing DFT will ever succeed for this system.
> 
> LDA: P. Duffy, D. P. Chong and M. Dupuis, J. Chem. Phys. 102, 3312 (1995)
> MRCI: J.F. Harrison, J. Phys. Chem. A 110, 10848-10857 (2006).
> CC/MP: Scuseria, et. al, J. Chem. Phys. 94, 6660-6663 (1991)
> CC/MP:K.A. Peterson and T.H. Dunning, Theochem 400, 93 (1997)
> 
> Jeff
> 
> On 12/6/06, DE BRUIN Theodorus theodorus.DE-BRUIN[*]IFP.fr
> <owner-chemistry^_^ccl.net> wrote:
> > Sent to CCL by: "DE BRUIN Theodorus" [theodorus.DE-BRUIN^-^IFP.fr]
> >
> > Dear CCLers
> >
> > It seems that some density functionals are not well predicting the dipole moment of the CO molecule. Although the magnitude has the correct order, the direction is wrong (oxygen atom is carrying the negative charge instead of the carbon atom). Moreover, upon increasing the basis set, e.g. from triple zeta to aug-cc-pvtz, the direction of the dipole may change as well.
> >
> > Could anyone of you point me to some articles in which functionals (and basis sets) were systematically tested for the CO molecule?
> >
> > Thanks in advance,
> > Kind regards,
> > Theo de Bruin
> >
> > --------
> > Theodorus de Bruin
> > Institut Français du Pétrole
> > Direction Chimie et Physico-Chimie Appliquées
> > Département Thermodynamique et Modélisation Moléculaire
> > 1 & 4 Avenue de bois Préau
> > 92852 Rueil-Malmaison Cedex
> > Tel: +33 (0)1.47.52.54.38
> > Fax: +33 (0)1.47.52.70.58
> >
> > __________________________
> >
> > Ce message (et toutes ses pièces jointes éventuelles) est confidentiel et établi à l'intention exclusive de ses destinataires. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse. L'IFP décline toute responsabilité au titre de ce message.
> >
> > This message and any attachments (the message) are confidential and intended solely for the addressees. Any unauthorised use or dissemination is prohibited. IFP should not be liable for this message.
> >
> > Visitez notre site Web / Visit our web site : http://www.ifp.fr
> > __________________________>
> >
> >
> >
> 
> 
> 
> 

-- 
<

    ..  .. ****************************************** ..  .. 
    ..  Prof. Dr. Patrizia Calaminici               .. 
   * Departamento de Quimica,                   *
   * CINVESTAV, Centro De Investigacion         *
   * Y De Estudios Avanzados,                   *
   * Av. Instituto Politecnico Nacional, 2508   *
   * A.P. 14-740 Mexico D.F. 07000              *
   * MEXICO                                     *
   * Tel: 5255-5-061-3911 (Office)              *
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From owner-chemistry@ccl.net Wed Dec  6 17:20:00 2006
From: "Tom Sundius Tom.Sundius[-]helsinki.fi" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Density functionals for CO molecule
Message-Id: <-33198-061206162443-21129-LZgUbrOyd3jbkMUFOlsmew!=!server.ccl.net>
X-Original-From: Tom Sundius <Tom.Sundius-#-helsinki.fi>
Content-Type: MULTIPART/MIXED; BOUNDARY="1824380544-2141119353-1165437414=:178871"
Date: Wed, 6 Dec 2006 22:36:54 +0200 (EET)
MIME-Version: 1.0


Sent to CCL by: Tom Sundius [Tom.Sundius ~ helsinki.fi]
  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

--1824380544-2141119353-1165437414=:178871
Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: QUOTED-PRINTABLE


It is well-known that SCF gives the wrong sign for the dipole moment
of CO, but that the inclusion of electron correlation reverses=20
its sign.  As shown in the paper by Peterson and Dunning (quoted below),
MP2 substantially overestimates overestimates the CO dipole moment even
for basis sets as large as aug-cc-pV5Z. However, in a paper by A.J. Cohen
and Y. Tantirungrotechai (Chem. Phys. Lett. 299 (1999) 465) it is shown
that DFT with suitably chosen hybrid functionals can give the CO dipole
moment in good agreement with the experimental results.

       Best regards,

        Tom S.

On Wed, 6 Dec 2006, Jeff Hammond jeff.science(0)gmail.com wrote:

> Sent to CCL by: "Jeff Hammond" [jeff.science---gmail.com]
> Most SCF-based calculations, which includes DFT, do not get the sign
> right, as you discovered.  Here are few papers which study the CO
> dipole moment, but only the first has a DFT number.  The rest should
> give you pause about believing DFT will ever succeed for this system.
>
> LDA: P. Duffy, D. P. Chong and M. Dupuis, J. Chem. Phys. 102, 3312 (1995)
> MRCI: J.F. Harrison, J. Phys. Chem. A 110, 10848-10857 (2006).
> CC/MP: Scuseria, et. al, J. Chem. Phys. 94, 6660-6663 (1991)
> CC/MP:K.A. Peterson and T.H. Dunning, Theochem 400, 93 (1997)
>
> Jeff
>
> On 12/6/06, DE BRUIN Theodorus theodorus.DE-BRUIN[*]IFP.fr
> <owner-chemistry^_^ccl.net> wrote:
>> Sent to CCL by: "DE BRUIN Theodorus" [theodorus.DE-BRUIN^-^IFP.fr]
>>
>> Dear CCLers
>>
>> It seems that some density functionals are not well predicting the dipol=
e moment of the CO molecule. Although the magnitude has the correct order, =
the direction is wrong (oxygen atom is carrying the negative charge instead=
 of the carbon atom). Moreover, upon increasing the basis set, e.g. from tr=
iple zeta to aug-cc-pvtz, the direction of the dipole may change as well.
>>
>> Could anyone of you point me to some articles in which functionals (and =
basis sets) were systematically tested for the CO molecule?
>>
>> Thanks in advance,
>> Kind regards,
>> Theo de Bruin
>>
>> --------
>> Theodorus de Bruin
>> Institut Fran=E7ais du P=E9trole
>> Direction Chimie et Physico-Chimie Appliqu=E9es
>> D=E9partement Thermodynamique et Mod=E9lisation Mol=E9culaire
>> 1 & 4 Avenue de bois Pr=E9au
>> 92852 Rueil-Malmaison Cedex
>> Tel: +33 (0)1.47.52.54.38
>> Fax: +33 (0)1.47.52.70.58
>>
>> __________________________
>>
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el et =E9tabli =E0 l'intention exclusive de ses destinataires. Toute utilis=
ation de ce message non conforme =E0 sa destination, toute diffusion ou tou=
te publication, totale ou partielle, est interdite, sauf autorisation expre=
sse. L'IFP d=E9cline toute responsabilit=E9 au titre de ce message.
>>
>> This message and any attachments (the message) are confidential and inte=
nded solely for the addressees. Any unauthorised use or dissemination is pr=
ohibited. IFP should not be liable for this message.
>>
>> Visitez notre site Web / Visit our web site : http://www.ifp.fr
>> __________________________>
>>
>>
>>
>
>
>
> --=20
> Jeff Hammond
> The University of Chicago
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
>
>
>

Tom Sundius
University of Helsinki, Dept of Physical Sciences   phone +358-9-191 50672
P.O.Box 64, FIN-00014 Helsinki, Finland             fax   +358-9-191 50610
+++ for we know in part, and we prophesy in part +++
--1824380544-2141119353-1165437414=:178871--


From owner-chemistry@ccl.net Wed Dec  6 19:02:00 2006
From: "Elaine Landwehr landwehr[]osc.edu" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry Grid (CCG) released its new GridChem client
Message-Id: <-33199-061206172946-5697-6lv08iB4xBHOXr6e1xueBw.@.server.ccl.net>
X-Original-From: "Elaine  Landwehr" <landwehr_+_osc.edu>
Date: Wed, 6 Dec 2006 17:29:46 -0500


Sent to CCL by: "Elaine  Landwehr" [landwehr-x-osc.edu]
GridChem Enhances Client With Web Services 

COLUMBUS, Ohio - December 6, 2006 - The Computational Chemistry Grid (CCG) released its new GridChem client today.  The beta release of the client has been available since mid-November.

The CCG client, GridChem, is a Java desktop application that runs on any platform as a chemistry workbench and interfaces to High Performance Computing (HPC) systems for quantum application execution.  The GridChem cyberinfrastructure integrates remote HPC systems,  applications, the desktop client, and  middleware grid technologies to create an intuitive, easy-to-use system for solving quantum chemistry problems. (www.gridchem.org)

We are proud of what our chemistry cyberinfrastructure can do for the scientific  community, said Dr. John Connolly, GridChem Principal Investigator and Director of the University of Kentucky Center for Computational Sciences.  The developers have accomplished a great deal since the project began in 2004.  We listened to our users and the resulting client -- along with the architectural changes that will accelerate adaptation of new services -- will be of great benefit to the community,  said Connolly.

Some features in the new client include:
- Secure, session-based interaction with the middleware
- Real-time accounting and usage information
- Automatic job status updates
- New, feature-rich resource and queue monitoring interface
- Redesigned file browser
- Native text editing of output files
- Full help documentation integrated within the client
- Resource status notifications (e.g. scheduled maintenance) delivered to client

For more information about the project and to download the new client, visit the GridChem website at http:// www.gridchem.org/.

GridChem partners include the Center for Computational Sciences / University of Kentucky, Center for Computation and Technology / Louisiana State University, National Center for Supercomputing Applications (NCSA) / University of Illinois 
Urbana-Champaign, OSC / The Ohio State University, and Texas Advanced Computing Center (TACC) / The University of Texas at Austin.  The project is supported by the National Science Foundation NMI Program under Award 04-38312.

For more information, contact:
Elaine Landwehr
614-292-0890
landwehr() osc.edu


From owner-chemistry@ccl.net Wed Dec  6 19:41:01 2006
From: "Dave Winkler dave.winkler a csiro.au" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Computational biology
Message-Id: <-33200-061206192310-22602-MTxAZt+X4LwM6c4pQFPJpA#server.ccl.net>
X-Original-From: Dave Winkler <dave.winkler+*+csiro.au>
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Date: Thu, 7 Dec 2006 09:52:42 +1100
Mime-Version: 1.0


Sent to CCL by: Dave Winkler [dave.winkler:_:csiro.au]
Dear Venkata,

I suggest you look at the papers published by Glen Kellogg from 
Virginia Commonwealth University.  He has done a lot of work in this 
area and would also be able to answer your questions
-- 
Cheers,
Dave

Prof. David A. Winkler FRACI CChem CPChem	Email: dave.winkler|,|csiro.au  
CSIRO Centre for Complexity in Drug Design 	Voice: 61-3-9545-2477
Senior Principal Research Scientist    		Fax:  61-3-9545-2561
CSIRO Molecular and Health Technologies	or 61-3-9545-2446
Private Bag 10,Clayton South MDC 3169 	http://www.csiro.au
Australia	       		 		http://www.molsci.csiro.au

Join us at Drug Design Amongst the Vines, Hunter Valley, Australia 
3-7 December 2006 (http://www.ddconference.com)


From owner-chemistry@ccl.net Wed Dec  6 22:25:00 2006
From: "Don Steiger sd00_2002!=!yahoo.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Computational biology
Message-Id: <-33201-061206201034-16548-reA0oZf32XcmeCSDfvihbg/./server.ccl.net>
X-Original-From: Don Steiger <sd00_2002 .. yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Wed, 6 Dec 2006 16:10:25 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Don Steiger [sd00_2002%a%yahoo.com]
I'm not an expert on the subject, but it's my
understanding that the r^6 term is basically an
approximation for dipole-dipole interactions.  The
coefficient for this term is picked to minimize the
error in some least squares sense.  The r^12 term
gives you the hard wall, and is generally considered
to be an extremely crude estimate of the repulsive
forces.  I suspect the main issue here is how well can
a constant coefficient to r^6 reflect the
dipole-dipole interactions of your system.


--- "venkat karanam dodaghatta
dkvenkata_rao()yahoo.co.in" <owner-chemistry{:}ccl.net>
wrote:

> Sent to CCL by: "venkat karanam dodaghatta"
> [dkvenkata_rao]^[yahoo.co.in]
> 
> Dear sir,
> 
> 
> I am Venkata Rao.D.K from India doing doctoral
> studies in computational biophysics. as a part of my
> research I have calculated lennard-jones potential
> between hydrophobic groups. my basic doubt is that
> can we define lennard-jones potential as hydrophobic
> energies or it is just approximation of vander waal
> interaction energies?.
> 
> is there any method to calculate hydrophobic
> interaction energies and any method to calculate
> continuum hydrophobic energies of energy files
> generated from MD.
> 
> please clarify my doubts
> 
> 
> 
> 
> > From
> VENKATA RAO.D.K
> Dept of Microbiology
> Sri Krishnadevaraya University
> ANANTAPUR-515001
> INDIA
> 
> E-mail: dkvenkata_rao]-[yahoo.co.in
>         dkvenkata_rao]-[sancharnet.in
> 
> 
> 
> -= This is automatically added to each message by
> the mailing script =-
> To recover the email address of the author of the
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> 
> 
> 


 
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From owner-chemistry@ccl.net Wed Dec  6 22:59:01 2006
From: "silviu polosan Spol68%%yahoo.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: dipole orientation
Message-Id: <-33202-061206225432-8305-U7BTm/qDUule9CV/ajahxQ(0)server.ccl.net>
X-Original-From: "silviu  polosan" <Spol68:+:yahoo.com>
Date: Wed, 6 Dec 2006 22:54:32 -0500


Sent to CCL by: "silviu  polosan" [Spol68**yahoo.com]
Hi all,

I want to calculate and especially to see the dipole orintation in the molecule. Can anyone tell me how to modify the current job?

Thanks a lot